niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3dfim_.py

@@ -0,0 +1,350 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DFIM__METADATA = Metadata(
+    id="bc809f4b3edfb691248a034084e93881b2cf1fd0.boutiques",
+    name="3dfim+",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dfimParameters = typing.TypedDict('V3dfimParameters', {
+    "__STYX_TYPE__": typing.Literal["3dfim+"],
+    "infile": InputPathType,
+    "input1dfile": typing.NotRequired[InputPathType | None],
+    "maskfile": typing.NotRequired[InputPathType | None],
+    "first_image": typing.NotRequired[float | None],
+    "last_image": typing.NotRequired[float | None],
+    "baseline_polynomial": typing.NotRequired[float | None],
+    "threshold": typing.NotRequired[float | None],
+    "cdisp_value": typing.NotRequired[float | None],
+    "ort_file": typing.NotRequired[InputPathType | None],
+    "ideal_file": InputPathType,
+    "output_params": typing.NotRequired[list[str] | None],
+    "output_bucket": typing.NotRequired[str | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dfim+": v_3dfim__cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+        "3dfim+": v_3dfim__outputs,
+    }.get(t)
+
+
+class V3dfimOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3dfim_(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile_tlrc_head: OutputPathType | None
+    """Output bucket dataset containing fit parameters, in TLRC space."""
+    outfile_tlrc_brk: OutputPathType | None
+    """Output bucket dataset containing fit parameters, in TLRC space."""
+    outfile_orig_head: OutputPathType | None
+    """Output bucket dataset containing fit parameters, in original space."""
+    outfile_orig_brk: OutputPathType | None
+    """Output bucket dataset containing fit parameters, in original space."""
+
+
+def v_3dfim__params(
+    infile: InputPathType,
+    ideal_file: InputPathType,
+    input1dfile: InputPathType | None = None,
+    maskfile: InputPathType | None = None,
+    first_image: float | None = None,
+    last_image: float | None = None,
+    baseline_polynomial: float | None = None,
+    threshold: float | None = None,
+    cdisp_value: float | None = None,
+    ort_file: InputPathType | None = None,
+    output_params: list[str] | None = None,
+    output_bucket: str | None = None,
+) -> V3dfimParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infile: Filename of input 3d+time dataset.
+        ideal_file: Input ideal time series file name. Can be used multiple\
+            times.
+        input1dfile: Filename of single (fMRI) .1D time series.
+        maskfile: Filename of 3d mask dataset.
+        first_image: Number of first dataset image to use in the\
+            cross-correlation procedure (default = 0).
+        last_image: Number of last dataset image to use in the\
+            cross-correlation procedure (default = last).
+        baseline_polynomial: Degree of polynomial corresponding to the baseline\
+            model (default: 1). Use -1 for no baseline model.
+        threshold: FIM internal mask threshold value (0 <= p <= 1) to get rid\
+            of low intensity voxels (default: 0.0999).
+        cdisp_value: Write (to screen) results for voxels whose correlation\
+            stat. > cval (0 <= cval <= 1; default: disabled).
+        ort_file: Input ort time series file name. Can be used multiple times.
+        output_params: Output the specified parameter. Can be used multiple\
+            times. Possible values are: 'Fit Coef', 'Best Index', '% Change',\
+            'Baseline', 'Correlation', '% From Ave', 'Average', '% From Top',\
+            'Topline', 'Sigma Resid', 'All', 'Spearman CC', 'Quadrant CC'.
+        output_bucket: Create one AFNI 'bucket' dataset containing the\
+            parameters of interest, as specified by the '-out' commands. The output\
+            'bucket' dataset is written to a file with the prefix name bprefix.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dfim+",
+        "infile": infile,
+        "ideal_file": ideal_file,
+    }
+    if input1dfile is not None:
+        params["input1dfile"] = input1dfile
+    if maskfile is not None:
+        params["maskfile"] = maskfile
+    if first_image is not None:
+        params["first_image"] = first_image
+    if last_image is not None:
+        params["last_image"] = last_image
+    if baseline_polynomial is not None:
+        params["baseline_polynomial"] = baseline_polynomial
+    if threshold is not None:
+        params["threshold"] = threshold
+    if cdisp_value is not None:
+        params["cdisp_value"] = cdisp_value
+    if ort_file is not None:
+        params["ort_file"] = ort_file
+    if output_params is not None:
+        params["output_params"] = output_params
+    if output_bucket is not None:
+        params["output_bucket"] = output_bucket
+    return params
+
+
+def v_3dfim__cargs(
+    params: V3dfimParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("3dfim+")
+    cargs.append(execution.input_file(params.get("infile")))
+    if params.get("input1dfile") is not None:
+        cargs.extend([
+            "-input1D",
+            execution.input_file(params.get("input1dfile"))
+        ])
+    if params.get("maskfile") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("maskfile"))
+        ])
+    if params.get("first_image") is not None:
+        cargs.extend([
+            "-nfirst",
+            str(params.get("first_image"))
+        ])
+    if params.get("last_image") is not None:
+        cargs.extend([
+            "-nlast",
+            str(params.get("last_image"))
+        ])
+    if params.get("baseline_polynomial") is not None:
+        cargs.extend([
+            "-polort",
+            str(params.get("baseline_polynomial"))
+        ])
+    if params.get("threshold") is not None:
+        cargs.extend([
+            "-fim_thr",
+            str(params.get("threshold"))
+        ])
+    if params.get("cdisp_value") is not None:
+        cargs.extend([
+            "-cdisp",
+            str(params.get("cdisp_value"))
+        ])
+    if params.get("ort_file") is not None:
+        cargs.extend([
+            "-ort_file",
+            execution.input_file(params.get("ort_file"))
+        ])
+    cargs.extend([
+        "-ideal_file",
+        execution.input_file(params.get("ideal_file"))
+    ])
+    if params.get("output_params") is not None:
+        cargs.extend([
+            "-out",
+            *params.get("output_params")
+        ])
+    if params.get("output_bucket") is not None:
+        cargs.extend([
+            "-bucket",
+            params.get("output_bucket")
+        ])
+    return cargs
+
+
+def v_3dfim__outputs(
+    params: V3dfimParameters,
+    execution: Execution,
+) -> V3dfimOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = V3dfimOutputs(
+        root=execution.output_file("."),
+        outfile_tlrc_head=execution.output_file(params.get("output_bucket") + "+tlrc.HEAD") if (params.get("output_bucket") is not None) else None,
+        outfile_tlrc_brk=execution.output_file(params.get("output_bucket") + "+tlrc.BRIK") if (params.get("output_bucket") is not None) else None,
+        outfile_orig_head=execution.output_file(params.get("output_bucket") + "+orig.HEAD") if (params.get("output_bucket") is not None) else None,
+        outfile_orig_brk=execution.output_file(params.get("output_bucket") + "+orig.BRIK") if (params.get("output_bucket") is not None) else None,
+    )
+    return ret
+
+
+def v_3dfim__execute(
+    params: V3dfimParameters,
+    execution: Execution,
+) -> V3dfimOutputs:
+    """
+    Program to calculate the cross-correlation of an ideal reference waveform with
+    the measured FMRI time series for each voxel.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dfimOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3dfim__cargs(params, execution)
+    ret = v_3dfim__outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3dfim_(
+    infile: InputPathType,
+    ideal_file: InputPathType,
+    input1dfile: InputPathType | None = None,
+    maskfile: InputPathType | None = None,
+    first_image: float | None = None,
+    last_image: float | None = None,
+    baseline_polynomial: float | None = None,
+    threshold: float | None = None,
+    cdisp_value: float | None = None,
+    ort_file: InputPathType | None = None,
+    output_params: list[str] | None = None,
+    output_bucket: str | None = None,
+    runner: Runner | None = None,
+) -> V3dfimOutputs:
+    """
+    Program to calculate the cross-correlation of an ideal reference waveform with
+    the measured FMRI time series for each voxel.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        infile: Filename of input 3d+time dataset.
+        ideal_file: Input ideal time series file name. Can be used multiple\
+            times.
+        input1dfile: Filename of single (fMRI) .1D time series.
+        maskfile: Filename of 3d mask dataset.
+        first_image: Number of first dataset image to use in the\
+            cross-correlation procedure (default = 0).
+        last_image: Number of last dataset image to use in the\
+            cross-correlation procedure (default = last).
+        baseline_polynomial: Degree of polynomial corresponding to the baseline\
+            model (default: 1). Use -1 for no baseline model.
+        threshold: FIM internal mask threshold value (0 <= p <= 1) to get rid\
+            of low intensity voxels (default: 0.0999).
+        cdisp_value: Write (to screen) results for voxels whose correlation\
+            stat. > cval (0 <= cval <= 1; default: disabled).
+        ort_file: Input ort time series file name. Can be used multiple times.
+        output_params: Output the specified parameter. Can be used multiple\
+            times. Possible values are: 'Fit Coef', 'Best Index', '% Change',\
+            'Baseline', 'Correlation', '% From Ave', 'Average', '% From Top',\
+            'Topline', 'Sigma Resid', 'All', 'Spearman CC', 'Quadrant CC'.
+        output_bucket: Create one AFNI 'bucket' dataset containing the\
+            parameters of interest, as specified by the '-out' commands. The output\
+            'bucket' dataset is written to a file with the prefix name bprefix.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dfimOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DFIM__METADATA)
+    params = v_3dfim__params(
+        infile=infile,
+        input1dfile=input1dfile,
+        maskfile=maskfile,
+        first_image=first_image,
+        last_image=last_image,
+        baseline_polynomial=baseline_polynomial,
+        threshold=threshold,
+        cdisp_value=cdisp_value,
+        ort_file=ort_file,
+        ideal_file=ideal_file,
+        output_params=output_params,
+        output_bucket=output_bucket,
+    )
+    return v_3dfim__execute(params, execution)
+
+
+__all__ = [
+    "V3dfimOutputs",
+    "V3dfimParameters",
+    "V_3DFIM__METADATA",
+    "v_3dfim_",
+    "v_3dfim__params",
+]

niwrap_afni/afni/v_3dfractionize.py

@@ -0,0 +1,261 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DFRACTIONIZE_METADATA = Metadata(
+    id="700df8ed70958c3087524da2a286d3508d1bd05d.boutiques",
+    name="3dfractionize",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dfractionizeParameters = typing.TypedDict('V3dfractionizeParameters', {
+    "__STYX_TYPE__": typing.Literal["3dfractionize"],
+    "template": InputPathType,
+    "input": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+    "clip": typing.NotRequired[float | None],
+    "warp": typing.NotRequired[InputPathType | None],
+    "preserve": bool,
+    "vote": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dfractionize": v_3dfractionize_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+        "3dfractionize": v_3dfractionize_outputs,
+    }.get(t)
+
+
+class V3dfractionizeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3dfractionize(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType | None
+    """Output dataset with the specified prefix."""
+
+
+def v_3dfractionize_params(
+    template: InputPathType,
+    input_: InputPathType,
+    prefix: str | None = None,
+    clip: float | None = None,
+    warp: InputPathType | None = None,
+    preserve: bool = False,
+    vote: bool = False,
+) -> V3dfractionizeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        template: Use dataset as a template for the output. The output dataset\
+            will be on the same grid as this dataset.
+        input_: Use dataset for the input. Only the sub-brick #0 of the input\
+            is used.
+        prefix: Prefix for the output dataset.
+        clip: Clip off voxels that are less than the specified occupancy\
+            fraction.
+        warp: Dataset that provides a transformation (warp) from +orig\
+            coordinates to the coordinates of the input dataset.
+        preserve: Preserve the nonzero values of input voxels in the output\
+            dataset rather than creating a fractional mask.
+        vote: Vote for which input value to preserve when using the preserve\
+            flag.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dfractionize",
+        "template": template,
+        "input": input_,
+        "preserve": preserve,
+        "vote": vote,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if clip is not None:
+        params["clip"] = clip
+    if warp is not None:
+        params["warp"] = warp
+    return params
+
+
+def v_3dfractionize_cargs(
+    params: V3dfractionizeParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("3dfractionize")
+    cargs.extend([
+        "-template",
+        execution.input_file(params.get("template"))
+    ])
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input"))
+    ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("clip") is not None:
+        cargs.extend([
+            "-clip",
+            str(params.get("clip"))
+        ])
+    if params.get("warp") is not None:
+        cargs.extend([
+            "-warp",
+            execution.input_file(params.get("warp"))
+        ])
+    if params.get("preserve"):
+        cargs.append("-preserve")
+    if params.get("vote"):
+        cargs.append("-vote")
+    return cargs
+
+
+def v_3dfractionize_outputs(
+    params: V3dfractionizeParameters,
+    execution: Execution,
+) -> V3dfractionizeOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = V3dfractionizeOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("prefix")) if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3dfractionize_execute(
+    params: V3dfractionizeParameters,
+    execution: Execution,
+) -> V3dfractionizeOutputs:
+    """
+    For each voxel in the output dataset, computes the fraction of it that is
+    occupied by nonzero voxels from the input.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dfractionizeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3dfractionize_cargs(params, execution)
+    ret = v_3dfractionize_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3dfractionize(
+    template: InputPathType,
+    input_: InputPathType,
+    prefix: str | None = None,
+    clip: float | None = None,
+    warp: InputPathType | None = None,
+    preserve: bool = False,
+    vote: bool = False,
+    runner: Runner | None = None,
+) -> V3dfractionizeOutputs:
+    """
+    For each voxel in the output dataset, computes the fraction of it that is
+    occupied by nonzero voxels from the input.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        template: Use dataset as a template for the output. The output dataset\
+            will be on the same grid as this dataset.
+        input_: Use dataset for the input. Only the sub-brick #0 of the input\
+            is used.
+        prefix: Prefix for the output dataset.
+        clip: Clip off voxels that are less than the specified occupancy\
+            fraction.
+        warp: Dataset that provides a transformation (warp) from +orig\
+            coordinates to the coordinates of the input dataset.
+        preserve: Preserve the nonzero values of input voxels in the output\
+            dataset rather than creating a fractional mask.
+        vote: Vote for which input value to preserve when using the preserve\
+            flag.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dfractionizeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DFRACTIONIZE_METADATA)
+    params = v_3dfractionize_params(
+        template=template,
+        input_=input_,
+        prefix=prefix,
+        clip=clip,
+        warp=warp,
+        preserve=preserve,
+        vote=vote,
+    )
+    return v_3dfractionize_execute(params, execution)
+
+
+__all__ = [
+    "V3dfractionizeOutputs",
+    "V3dfractionizeParameters",
+    "V_3DFRACTIONIZE_METADATA",
+    "v_3dfractionize",
+    "v_3dfractionize_params",
+]